NP-MRD: Showing NP-Card for Virgilidone (NP0067581)

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Record Information

Version

2.0

Created at

2022-04-28 12:26:36 UTC

Updated at

2022-04-28 12:26:36 UTC

NP-MRD ID

NP0067581

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Virgilidone

Description

Virgilidone belongs to the class of organic compounds known as quinolizidinones. Quinolizidinones are compounds containing a quinolizidine moiety which bears a ketone group. Virgilidone is found in Virgilia 3 species and Virgilia oroboides. Based on a literature review very few articles have been published on Virgilidone.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 34  0  0  0  0  0  0  0  0999 V2000
    0.0002    1.1950    2.7248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3051    0.4807    1.7101 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7298    0.1785    1.4164 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3080    1.3327    0.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7935    0.8630   -0.6753 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6065    0.3602   -1.3847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0713   -0.8536   -0.6837 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8138   -1.0923    0.6373 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3800   -0.7865   -0.3612 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2260   -0.3105   -1.5252 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6707   -0.5413   -1.0694 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9251    0.5264   -0.0101 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0695    0.1821    1.1754 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6859   -0.0441    0.8373 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2986    0.1009    2.3650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0833    1.8671    1.1873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5102    2.0886    0.3732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4918    0.1123   -0.6047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9441    0.1403   -2.4282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8699    1.1823   -1.3887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2356   -1.7511   -1.3276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8209   -1.4749    0.4874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2148   -1.8707    1.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7215   -1.8448   -0.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0979    0.7666   -1.7285 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9850   -0.9500   -2.3891 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7110   -1.5176   -0.5393 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3812   -0.4951   -1.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6243    1.5254   -0.3898 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9733    0.4806    0.2843 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1764    0.9358    1.9941 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4692   -0.7856    1.5873 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14  2  1  0
  8  3  1  0
 14  9  1  0
  3 15  1  1
  4 16  1  0
  4 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  6
  8 22  1  0
  8 23  1  0
  9 24  1  1
 10 25  1  0
 10 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 13 32  1  0
M  END


  Mrv1652304282214262D          

 14 16  0  0  1  0            999 V2000
    0.3115    0.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2416   -0.2113    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7734   -0.8420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5954   -0.9119    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2261   -0.3801    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2961    0.4419    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7643    1.0726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1435    1.8053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9423    1.1426    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0120    0.0337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0430    0.7923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7199    0.3207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6499   -0.5013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9031   -0.8517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  1  9  1  0  0  0  0
  9 10  1  1  0  0  0
  4 10  1  1  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  5 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0067581

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1[C@H]2CNC[C@H](C2)[C@H]2CCCCN12

> <INCHI_IDENTIFIER>
InChI=1S/C11H18N2O/c14-11-9-5-8(6-12-7-9)10-3-1-2-4-13(10)11/h8-10,12H,1-7H2/t8-,9+,10+/m0/s1

> <INCHI_KEY>
JTEWAGIMBZUVTB-IVZWLZJFSA-N

> <FORMULA>
C11H18N2O

> <MOLECULAR_WEIGHT>
194.278

> <EXACT_MASS>
194.141913208

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
21.489276711854544

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,9R)-7,11-diazatricyclo[7.3.1.0^{2,7}]tridecan-8-one

> <ALOGPS_LOGP>
0.69

> <JCHEM_LOGP>
0.07511035799999961

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.676415678071738

> <JCHEM_POLAR_SURFACE_AREA>
32.34

> <JCHEM_REFRACTIVITY>
54.38930000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.56e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,9R)-7,11-diazatricyclo[7.3.1.0^{2,7}]tridecan-8-one

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       0.582   1.140   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.451  -0.394   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       1.444  -1.572   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.978  -1.702   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.155  -0.710   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.286   0.825   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.293   2.002   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001   3.370   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.759   2.133   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.889   0.063   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.680   1.479   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.944   0.599   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.813  -0.936   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.419  -1.590   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7   11                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    1   10                                                  
CONECT   10    9    4                                                       
CONECT   11    6   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    5                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₈N₂O

Average Mass

194.2780 Da

Monoisotopic Mass

194.14191 Da

IUPAC Name

(1S,2R,9R)-7,11-diazatricyclo[7.3.1.0^{2,7}]tridecan-8-one

Traditional Name

(1S,2R,9R)-7,11-diazatricyclo[7.3.1.0^{2,7}]tridecan-8-one

CAS Registry Number

Not Available

SMILES

O=C1[C@H]2CNC[C@H](C2)[C@H]2CCCCN12

InChI Identifier

InChI=1S/C11H18N2O/c14-11-9-5-8(6-12-7-9)10-3-1-2-4-13(10)11/h8-10,12H,1-7H2/t8-,9+,10+/m0/s1

InChI Key

JTEWAGIMBZUVTB-IVZWLZJFSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Virgilia 3 species	Plant	KNApSAcK
Virgilia oroboides	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quinolizidinones. Quinolizidinones are compounds containing a quinolizidine moiety which bears a ketone group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolizidines

Sub Class

Quinolizidinones

Direct Parent

Quinolizidinones

Alternative Parents

Substituents

Beta amino acid or derivatives
Quinolizidinone
Delta-lactam
Piperidinone
Piperidine
Tertiary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Lactam
Secondary aliphatic amine
Carboxylic acid derivative
Azacycle
Secondary amine
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Amine
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	0.69	ALOGPS
logP	0.075	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Basic)	9.68	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	32.34 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	54.39 m³·mol⁻¹	ChemAxon
Polarizability	21.49 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00025371

Chemspider ID

9450581

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11275581

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Virgilidone (NP0067581)

MOL for NP0067581 (Virgilidone)

3D MOL for NP0067581 (Virgilidone)

3D SDF for NP0067581 (Virgilidone)

3D-SDF for NP0067581 (Virgilidone)

PDB for NP0067581 (Virgilidone)

3D PDB for NP0067581 (Virgilidone)

SMILES for NP0067581 (Virgilidone)

INCHI for NP0067581 (Virgilidone)

Structure for NP0067581 (Virgilidone)

3D Structure for NP0067581 (Virgilidone)